39
sequencing technologies such as Roche 454, Illumina, and Applied Biosystem
SOLiD
TM
rendered proper understanding of complete genome sequencing without
using traditional PCR or cloning. Because almost 99% of the microbes in various
environments are still far being cultured in media, metagenomics offers a path to
identify the complete microbiome profile, phylogenetic relationship, species diversity and abundance, metabolic abilities, and functional characteristics of the inhabiting microbes (Shah et al. 2011). Metagenomic approaches have emerged as a hub
for understanding the ecological and evolutionary record of microorganisms, which
is perhaps the most important, vital, and less explored biological area because of the
diverse millions of metagenomic reads and their functional implications (Gilbert
et al. 2011; Zarraonaindia et al. 2013) (Fig. 4.2).
NGS has facilitated high-speed generation of huge sequence data that can decipher the real picture of soil microbes in water, root rhizosphere, rhizoplane, and
phylloplane, and the body of humans, especially the gut, animals, fishes, insects,
and other organisms (Shokrall et al. 2012; Bai et al. 2014; Hanning and DiazSanchez 2015). Metagenomic data signify functional attributes of complex belowground microbes, their intra- and interactions and ecological services and thus help
to understand ecological and evolutionary aspects of the microbial ecosystems as
genetic and metabolic networks (Filippo et al. 2012; Ponomarova and Patil 2015).
Complex metagenomes can reflect how ecosystems are functioning and how biotic
and abiotic changes in the environment influence whole community functions in the
ecosystem. Thus, sequence assembly, annotation, analysis, phylogenetic surveys
from the metagenome data, gene-centric approaches, and functional characterization of microbial communities have remained major challenges for metagenomic
data analysis using bioinformatics protocols, pipelines, and data handling tools
(Thomas et al. 2012; Wooley and Ye 2009).
4.2.1 Metagenomics and Soil Microbial Diversity
Soil contains 10
8
−10
10
microbial cells per gram (Raynaud and Nunan 2014) that
accomplish life-sustaining functions for the planet. Soil is a biological entity that
remains largely unexplored although we know a little about its rich diversity of
microbial life (Liu et al. 2016a). Soil contains billions to trillions of microbial cells
per gram, including diverse species of bacteria, fungus, archaea, viruses, and unicellular protists (Jansson 2011) that are involved in nutrient turnover and improve plant
biomass and productivity (Prakash et al. 2014). Suppressive soils are one such
example in which plants stay healthy in the presence of a high density of diseasecausing organisms, although less is known about this phenomenon (MaldonadoMendoza et al. 2009). Metagenomics provides a distinctive opportunity to investigate
how microbial communities interact with crops to harness their potential for producing healthier and robust crops (Melcher et al. 2014). Metagenomic studies navigate the functional characteristics of belowground microbiomes and provide
in-depth understanding over the genetically conserved rRNA gene-based
phylogenetics (Cong et al. 2015; Rastogi and Sani 2011).
4.2 Metagenomics
sequencing technologies such as Roche 454, Illumina, and Applied Biosystem
SOLiD
TM
rendered proper understanding of complete genome sequencing without
using traditional PCR or cloning. Because almost 99% of the microbes in various
environments are still far being cultured in media, metagenomics offers a path to
identify the complete microbiome profile, phylogenetic relationship, species diversity and abundance, metabolic abilities, and functional characteristics of the inhabiting microbes (Shah et al. 2011). Metagenomic approaches have emerged as a hub
for understanding the ecological and evolutionary record of microorganisms, which
is perhaps the most important, vital, and less explored biological area because of the
diverse millions of metagenomic reads and their functional implications (Gilbert
et al. 2011; Zarraonaindia et al. 2013) (Fig. 4.2).
NGS has facilitated high-speed generation of huge sequence data that can decipher the real picture of soil microbes in water, root rhizosphere, rhizoplane, and
phylloplane, and the body of humans, especially the gut, animals, fishes, insects,
and other organisms (Shokrall et al. 2012; Bai et al. 2014; Hanning and DiazSanchez 2015). Metagenomic data signify functional attributes of complex belowground microbes, their intra- and interactions and ecological services and thus help
to understand ecological and evolutionary aspects of the microbial ecosystems as
genetic and metabolic networks (Filippo et al. 2012; Ponomarova and Patil 2015).
Complex metagenomes can reflect how ecosystems are functioning and how biotic
and abiotic changes in the environment influence whole community functions in the
ecosystem. Thus, sequence assembly, annotation, analysis, phylogenetic surveys
from the metagenome data, gene-centric approaches, and functional characterization of microbial communities have remained major challenges for metagenomic
data analysis using bioinformatics protocols, pipelines, and data handling tools
(Thomas et al. 2012; Wooley and Ye 2009).
4.2.1 Metagenomics and Soil Microbial Diversity
Soil contains 10
8
−10
10
microbial cells per gram (Raynaud and Nunan 2014) that
accomplish life-sustaining functions for the planet. Soil is a biological entity that
remains largely unexplored although we know a little about its rich diversity of
microbial life (Liu et al. 2016a). Soil contains billions to trillions of microbial cells
per gram, including diverse species of bacteria, fungus, archaea, viruses, and unicellular protists (Jansson 2011) that are involved in nutrient turnover and improve plant
biomass and productivity (Prakash et al. 2014). Suppressive soils are one such
example in which plants stay healthy in the presence of a high density of diseasecausing organisms, although less is known about this phenomenon (MaldonadoMendoza et al. 2009). Metagenomics provides a distinctive opportunity to investigate
how microbial communities interact with crops to harness their potential for producing healthier and robust crops (Melcher et al. 2014). Metagenomic studies navigate the functional characteristics of belowground microbiomes and provide
in-depth understanding over the genetically conserved rRNA gene-based
phylogenetics (Cong et al. 2015; Rastogi and Sani 2011).
4.2 Metagenomics